Publications

Last updated January 2023

• Akerman: Cell Reports 42:112280 (2023). Prorok P, et al. Loss of Ezh2 function remodels the DNA replication initiation landscape.
• Akerman: Cell Reports 35:108981 (2021). Akerman I, et al. Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene.
• Akerman: Nature Commun 11:4826 (2020). Akerman I, et al. A predictable conserved DNA base composition signature defines human core DNA replication origins.
• Badenhorst: Life Sci Alliance 3 (2020). Kwon SY, et al. Oxidised metabolites of the omega-6 fatty acid linoleic acid activate dFOXO.
• Bonifer: Nature Commun 14:267 (2023). Edginton-White B, et al. A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification.
• Bonifer: Life Science Alliance 4: e202000864 (2021). Kellaway SG, et al. Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories.
• Bonifer: Cancer Cell 34:674-689 e678 (2018). de Boer B, et al. Prospective Isolation and Characterization of Genetically and Functionally Distinct AML Subclones.
• Bonifer: Cancer Cell 34:626-642 e628 (2018). Martinez-Soria N, et al. The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation.
• Brogna: ELife 8: e41444 (2019). Singh AK, et al. The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci.
• Carlomagno: J Mol Biol:435: 167997 (2023). Kruger G, et al. An NMR Study of a 300-kDa AAA+ Unfoldase. doi: 10.1016/j.jmb.2023.167997
• Carlomagno: Structure 31:128-137 e125 (2023). Wang Y, et al. Structural insights into the activity regulation of full-length non-structural protein 1 from SARS-CoV-2.
• Cazier: JAMA Netw Open 5:e220130 (2022). Varnai C, et al. Mortality Among Adults With Cancer Undergoing Chemotherapy or Immunotherapy and Infected With COVID-19.
• Cockerill: EMBO J:e105220 (2020). Bevington SL, et al. IL-2/IL-7-inducible factors pioneer the path to T cell differentiation in advance of lineage-defining factors.
• Cockerill: Cell Reports 31:107748 (2020). Bevington SL, et al. Chromatin Priming Renders T Cell Tolerance-Associated Genes Sensitive to Activation below the Signaling Threshold for Immune Response Genes.
• Cockerill: EMBO J 35:515-535 (2016). Bevington SL, et al. Inducible chromatin priming is associated with the establishment of immunological memory in T cells.
• Cockerill and Bonifer: Nature Genetics 51:151-162 (2019). Assi SA, et al. Subtype-specific regulatory network rewiring in acute myeloid leukemia.
• Colbourne: Nature Commun 12:4306 (2021). Chaturvedi A, et al. Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia.
• Colbourne: PLoS Genetics 16:e1008518 (2020). Rago A, et al. Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis.
• Davies: Nature Commun 12:6313 (2021). Sanchez-Bailon MP, et al. Arginine methylation and ubiquitylation crosstalk controls DNA end-resection and homologous recombination repair.
• Davies: Cell Reports 21:3498-3513 (2017). Chiang K, et al. PRMT5 Is a Critical Regulator of Breast Cancer Stem Cell Function via Histone Methylation and FOXP1 Expression.
• Davies: Molecular Cell 65:900-916 e907 (2017). Clarke TL, et al. PRMT5-Dependent Methylation of the TIP60 Coactivator RUVBL1 Is a Key Regulator of Homologous Recombination.
• Frampton: Blood 141:1858-1870 (2023). Clarke ML, et al. MYB insufficiency disrupts proteostasis in hematopoietic stem cells, leading to age-related neoplasia.
• Frampton: Leukemia 31:957-966 (2017). Clarke M, et al. Transcriptional regulation of SPROUTY2 by MYB influences myeloid cell proliferation and stem cell properties by enhancing responsiveness to IL-3.
• Frampton: Sci Rep 7:11148 (2017). Volpe G, et al. Prognostic significance of high GFI1 expression in AML of normal karyotype and its association with a FLT3-ITD signature.
• Gambus: Molecular Cell Oct 10:S1097-2765(23)00761-X (ahead of print) (2023). Cvetkovic MA, et al. The structural mechanism of dimeric DONSON in replicative helicase activation. https://doi.org/10.1016/j.molcel.2023.09.029
• Gambus: J Biol Chem 298:102234 (2022). Tarcan Z, et al. The p97 segregase cofactor Ubxn7 facilitates replisome disassembly during S-phase Gambus: Life Science Alliance e201900390 (2019) Priego Moreno S, et al Mitotic replisome disassembly depends on TRAIP ubiquitin ligase activity.
• Gambus: Nature Cell Biology 18:468-479(2018). Sonneville R, et al. CUL-2LRR-1 and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis.
• Gambus: Nature Cell Biol 19:468-479 (2017). Sonneville R, et al. CUL-2LRR-1 and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis.
• Garcia: Elife 11 (2022). Vilaplana-Lopera N, et al. Crosstalk between AML and stromal cells triggers acetate secretion through the metabolic rewiring of stromal cells.
• Garcia: EMBO Rep 22:e51120 (2021). Blakemore D, et al. MYBL2 and ATM suppress replication stress in pluripotent stem cells.
• Garcia: Cancer Res (2018). Bayley R, et al. MYBL2 supports DNA double strand break repair in haematopoietic stem cells.
• Garcia: Cell Reports 24:1496-1511 e1498 (2018). Ward C, et al. Fine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic Reprogramming.
• Gendoo: Nature Commun 13:6323 (2022). van Leeuwen JE, et al. Computational pharmacogenomic screen identifies drugs that potentiate the anti-breast cancer activity of statins.
• Gendoo: PLoS Comput Biol 15:e1006596 (2019). Gendoo DMA, et al. Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer.
• Grzechnik: Hum Mol Genet (2022). Sledziowska M, et al. Non-coding RNAs associated with Prader-Willi syndrome regulate transcription of neurodevelopmental genes in human induced pluripotent stem cells.
• Grzechnik: Nature Commun 9: 1783 (2018). Nuclear fate of yeast snoRNA is determined by co-transcriptional Rnt1 cleavage.
• Higgs: Molecular Cell 82:1924-1939 e1910 (2022). Bayley R, et al. H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ.
• Higgs: Molecular Cell 71:25-41 e26 (2018). Higgs MR, et al. Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2.
• Ma: J Cell Biol 222: e202201137 (2023). Klucnika A, et al. REC drives recombination to repair double-strand breaks in animal mtDNA. doi: 10.1083/jcb.202201137
• Ma: Proc Natl Acad Sci U S A 120:e2306073120 (2023). Li AYZ, et al. Milton assembles large mitochondrial clusters, mitoballs, to sustain spermatogenesis.
• De Magalhaes: BMC Bioinformatics 23:10 (2022). Vega Magdaleno GD, et al. Machine learning-based predictions of dietary restriction associations across ageing-related genes.
• De Magalhaes: Nat Commun 12:2345 (2021). Chatsirisupachai K, et al. An integrative analysis of the age-associated multi-omic landscape across cancers.
• De Magalhaes: Genome Biol 21:91 (2020). Avelar RA, et al. A multidimensional systems biology analysis of cellular senescence in aging and disease.
• Moradigaravand: mSphere 6 (2021). Murphy R, et al. Genomic Epidemiology and Evolution of Escherichia coli in Wild Animals in Mexico.
• Moradigaravand: PLoS Comput Biol 14:e1006258 (2018). Moradigaravand D, et al. Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.
• Monteiro: Cell Reports 42:112571 (2023). Mahony CB et al. Lineage skewing and genome instability underlie marrow failure in a zebrafish model of GATA2 deficiency.
• Monteiro: Commun Biol 3:71 (2020). Dobrzycki T, et al. Deletion of a conserved Gata2 enhancer impairs haemogenic endothelium programming and adult Zebrafish haematopoiesis.
• Morris: J Cell Sci 135 (2022). Faulkner EL, et al. Imaging nanoscale nuclear structures with expansion microscopy.
• Morris: Nature 571:521-527 (2019). Daza-Martin M, et al. Isomerization of BRCA1-BARD1 promotes replication fork protection.
• Morris: Genes Dev 33:333-347 (2019). Garvin et al. The deSUMOylase SENP2 coordinates homologous recombination and nonhomologous end joining by independent mechanisms.
• Mueller: Developmental Cell 58:155-170 e158 (2023). Hadzhiev Y et al. The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation.
• Mueller: Nature Genet 54:1037-1050 (2022). Baranasic D, et al. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
• Mueller: Developmental Cell 56:641-656 e645 (2021). D'Orazio FM, et al. Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization.
• Mueller: Nature Commun 11:168 (2020). Nepal C, et al. Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing.
• Mueller: Nucleic Acids Res 48:8374-8392 (2020). Wragg JW, et al. Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation.
• Mueller: Nature Commun 10:691(2019). Hadzhiev Y, et al. A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation.
• Palles: Am J Hum Genet 109:953-960 (2022). Palles C, et al. Germline MBD4 deficiency causes a multi-tumor predisposition syndrome.
• Parish: PLoS Pathog 17:e1010032 (2021). Ferguson J, et al. The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression.
• Parish: PLoS Biology 16: e2005752 (2018).Pentland I, et al. Disruption of CTCF-YY1-dependent looping of the human papillomavirus genome activates differentiation-induced viral oncogene transcription.
• Parish :J Virol 91: e02305-16 (2017). Campos-Leon K, et al. Association of Human Papillomavirus 16 E2 with Rad50-Interacting Protein 1 Enhances Viral DNA Replication.
• Parish and Roberts: J Virol 91(1). pii: e01853-16 (2017). Harris L, et al. The Cellular DNA Helicase ChlR1 Regulates Chromatin and Nuclear Matrix Attachment of the Human Papillomavirus 16 E2 Protein and High-Copy-Number Viral Genome Establishment.
• Parsons: Front Oncol 12:940377 (2022). Zhou C, et al. Effectiveness of PARP inhibition in enhancing the radiosensitivity of 3D spheroids of head and neck squamous cell carcinoma.
• Parsons: Nucleic Acids Res 48:1301-1313 (2020). Bennett L, et al. HECTD1 promotes base excision repair in nucleosomes through chromatin remodelling.
• Parsons: Mol Cell Biol 38 (2018). Williams SC, Parsons JL NTH1 Is a New Target for Ubiquitylation-Dependent Regulation by TRIM26 Required for the Cellular Response to Oxidative Stress.
• Petermann: Cell Reports 25:2061-2069(2018). Bowry A, et al. BET Inhibition Induces HEXIM1- and RAD51-Dependent Conflicts between Transcription and Replication
• Petermann: Nature Commun 9:746 (2018). Ronson GE, et al. PARP1 and PARP2 stabilise replication forks at base excision repair intermediates through Fbh1-dependent Rad51 regulation.
• Saponaro: Cell Reports 34:108759 (2021). Wang J, et al. Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M.
• Saponaro: Cell 168:843-855 e813 (2017). Williamson L, et al. UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene.
• Soller: Nature Commun 13:1209 (2022). Haussmann IU, et al. CMTr cap-adjacent 2'-O-ribose mRNA methyltransferases are required for reward learning and mRNA localization to synapses.
• Soller: Commun Biol 4:1234 (2021). Ustaoglu P, et al. Dynamically expressed single ELAV/Hu orthologue elavl2 of bees is required for learning and memory.
• Stankovic: Nature 559:285-289 (2018). Zimmermann M, et al. CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions.
• Stewart: Nature Commun 13:6664 (2022). Grange LJ, et al. Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy.
• Stewart: J Clin Invest 132 (2022). Abu-Libdeh B, et al. RECON syndrome is a genome instability disorder caused by mutations in the DNA helicase RECQL1.
• Stewart: Nature Commun 11:3951 (2020). Zhang J, et al. DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain.
• Stewart: Nature Genetics 49:537-549 (2017). Reynolds JJ et al. DONSON encodes a novel replication fork protection factor mutated in microcephalic dwarfism.
• Tsai: Nature 570:117-121 (2019). Tsai HJ, et al. Hypo-osmotic-like stress underlies general cellular defects of aneuploidy.